/usr/share/arc/submit-lsf-job is in nordugrid-arc-arex 1.1.1-1.
This file is owned by root:root, with mode 0o755.
The actual contents of the file can be viewed below.
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# set -xv
#
# Submits job to LSF
# Input: path to grami file (same as Globus).
#
# A temporary job script is created for the submission and then removed
# at the end of this script.
echo "----- starting submit_lsf_job -----" 1>&2
joboption_lrms=lsf
# ARC1 passes first the config file.
if [ "$1" = "--config" ]; then shift; ARC_CONFIG=$1; shift; fi
basedir=`dirname $0`
basedir=`cd $basedir > /dev/null && pwd` || exit $?
pkgdatadir="$basedir"
##############################################################
# Set LSF specific environment. # relies on $joboption_queue #
##############################################################
. ${pkgdatadir}/configure-lsf-env.sh || exit $?
. ${pkgdatadir}/submit_common.sh || exit $?
##############################################################
# Parse grami file, read arc config
##############################################################
init $1
read_arc_conf
# enforce this
#RUNTIME_FRONTEND_SEES_NODE='yes'
#RUNTIME_NODE_SEES_FRONTEND='yes'
#TODO should this be specified here?
joboption_localtransfer='no'
##############################################################
# Zero stage of runtime environments
##############################################################
RTE_stage0
##############################################################
# create temp job script
##############################################################
mktempscript
##############################################################
# Start job script
##############################################################
LSF_BSUB='bsub'
if [ ! -z "$LSF_BIN_PATH" ] ; then
LSF_BSUB=${LSF_BIN_PATH}/${LSF_BSUB}
fi
echo "#! /bin/bash" > $LRMS_JOB_SCRIPT
echo "#LSF batch job script built by grid-manager" >> $LRMS_JOB_SCRIPT
echo "#" >> $LRMS_JOB_SCRIPT
# Specify the bash shell as default
#echo "#BSUB -L /bin/bash" >> $LRMS_JOB_SCRIPT
# Write output to comment file:
echo "#BSUB -oo ${joboption_directory}.comment" >> $LRMS_JOB_SCRIPT
echo "" >> $LRMS_JOB_SCRIPT
# Choose queue(s).
if [ ! -z "${joboption_queue}" ] ; then
echo "#BSUB -q $joboption_queue" >> $LRMS_JOB_SCRIPT
fi
if [ ! -z "${joboption_rsl_architecture}" ] ; then
queuearch=`echo ${joboption_rsl_architecture}|sed 's/\"//g'`
echo "#BSUB -R type=${queuearch}" >> $LRMS_JOB_SCRIPT
else
if [ ! -z $CONFIG_lsf_architecture ] ; then
echo "#BSUB -R type=$CONFIG_lsf_architecture" >> $LRMS_JOB_SCRIPT
fi
fi
# Project name for accounting
if [ ! -z "${joboption_rsl_project}" ] ; then
echo "#BSUB -P $joboption_rsl_project" >> $LRMS_JOB_SCRIPT
fi
# job name for convenience
if [ ! -z "${joboption_jobname}" ] ; then
jobname=`echo "$joboption_jobname" | \
sed 's/^\([^[:alpha:]]\)/N\1/' | \
sed 's/[^[:alnum:]]/_/g' | \
sed 's/\(...............\).*/\1/'`
echo "#BSUB -J $jobname" >> $LRMS_JOB_SCRIPT
fi
echo "LSF jobname: $jobname" 1>&2
##############################################################
# (non-)parallel jobs
##############################################################
if [ -z "$joboption_count" ] || [ "$joboption_count" -le 1 ] ; then
joboption_count=1
fi
##############################################################
# parallel jobs
##############################################################
echo "#BSUB -n $joboption_count" >> $LRMS_JOB_SCRIPT
##############################################################
# Execution times (obtained in seconds)
##############################################################
#OBS: Assuming here that LSB_JOB_CPULIMIT=y or is unset.
if [ -n "$joboption_cputime" ] && [ $joboption_cputime -gt 0 ]; then
cputime=$(( ${joboption_cputime} / 60 ))
echo "#BSUB -c ${cputime}" >> $LRMS_JOB_SCRIPT
fi
if [ -n "$joboption_walltime" ] && [ $joboption_walltime -gt 0 ] ; then
walltime=$(( ${joboption_walltime} / 60 ))
echo "#BSUB -W ${walltime}" >> $LRMS_JOB_SCRIPT
fi
##############################################################
# Requested memory (mb)
##############################################################
set_req_mem
if [ ! -z "$joboption_memory" ]; then
memory=$(( ${joboption_memory} * 1024 ))
echo "#BSUB -M ${memory}" >> $LRMS_JOB_SCRIPT
fi
##############################################################
# Start Time
##############################################################
if [ -n "$joboption_starttime" ] ; then
echo "#BSUB -b ${joboption_starttime}" >> $LRMS_JOB_SCRIPT
fi
##############################################################
# Override umask
##############################################################
echo "# Overide umask of execution node (sometime values are really strange)" >> $LRMS_JOB_SCRIPT
echo "umask 077" >> $LRMS_JOB_SCRIPT
##############################################################
# Add environment variables
##############################################################
add_user_env
##############################################################
# Check for existence of executable,
# there is no sense to check for executable if files are
# downloaded directly to computing node
##############################################################
if [ -z "${joboption_arg_0}" ] ; then
echo 'Executable is not specified' 1>&2
rm -f "$LRMS_JOB_SCRIPT" "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
echo "Submission: Job description error.">>"$failures_file"
exit 1
fi
if [ ! "$joboption_localtransfer" = 'yes' ] ; then
program_start=`echo ${joboption_arg_0} | head -c 1 2>&1`
if [ "$program_start" != '$' ] && [ "$program_start" != '/' ] ; then
if [ ! -f $joboption_directory/${joboption_arg_0} ] ; then
echo 'Executable does not exist, or permission denied.' 1>&2
echo " Executable $joboption_directory/${joboption_arg_0}" 1>&2
echo " whoami: "`whoami` 1>&2
echo " ls -l $joboption_directory/${joboption_arg_0}: "`ls -l $joboption_directory/${joboption_arg_0}`
exit 1
fi
if [ ! -x $joboption_directory/${joboption_arg_0} ] ; then
echo 'Executable is not executable' 1>&2
exit 1
fi
fi
fi
#######################################################################
# copy information useful for transfering files to/from node directly
#######################################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
setup_local_transfer
fi
######################################################################
# Adjust working directory for tweaky nodes
# RUNTIME_GRIDAREA_DIR should be defined by external means on nodes
######################################################################
if [ ! -z "${RUNTIME_NODE_SEES_FRONTEND}" ] ; then
setup_runtime_env
else
echo "RUNTIME_JOB_DIR=$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid" >> $LRMS_JOB_SCRIPT
echo "RUNTIME_JOB_DIAG=$RUNTIME_LOCAL_SCRATCH_DIR/${joboption_gridid}.diag" >> $LRMS_JOB_SCRIPT
RUNTIME_STDIN_REL=`echo "${joboption_stdin}" | sed "s#^${joboption_directory}/*##"`
RUNTIME_STDOUT_REL=`echo "${joboption_stdout}" | sed "s#^${joboption_directory}/*##"`
RUNTIME_STDERR_REL=`echo "${joboption_stderr}" | sed "s#^${joboption_directory}/*##"`
if [ "$RUNTIME_STDIN_REL" = "${joboption_stdin}" ] ; then
echo "RUNTIME_JOB_STDIN=\"${joboption_stdin}\"" >> $LRMS_JOB_SCRIPT
else
echo "RUNTIME_JOB_STDIN=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDIN_REL\"" >> $LRMS_JOB_SCRIPT
fi
if [ "$RUNTIME_STDOUT_REL" = "${joboption_stdout}" ] ; then
echo "RUNTIME_JOB_STDOUT=\"${joboption_stdout}\"" >> $LRMS_JOB_SCRIPT
else
echo "RUNTIME_JOB_STDOUT=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDOUT_REL\"" >> $LRMS_JOB_SCRIPT
fi
if [ "$RUNTIME_STDERR_REL" = "${joboption_stderr}" ] ; then
echo "RUNTIME_JOB_STDERR=\"${joboption_stderr}\"" >> $LRMS_JOB_SCRIPT
else
echo "RUNTIME_JOB_STDERR=\"$RUNTIME_LOCAL_SCRATCH_DIR/$joboption_gridid/$RUNTIME_STDERR_REL\"" >> $LRMS_JOB_SCRIPT
fi
fi
##############################################################
# Add std... to job arguments
##############################################################
include_std_streams
##############################################################
# Move files to local working directory (job is done on node only)
# RUNTIME_JOB_DIR -> RUNTIME_LOCAL_SCRATCH_DIR/job_id
##############################################################
move_files_to_node
echo "" >> $LRMS_JOB_SCRIPT
echo "RESULT=0" >> $LRMS_JOB_SCRIPT
echo "" >> $LRMS_JOB_SCRIPT
#####################################################
# Download input files
####################################################
download_input_files
#####################################################
# Go to working dir and start job
####################################################
echo "# Changing to session directory" >> $LRMS_JOB_SCRIPT
echo "cd \$RUNTIME_JOB_DIR" >> $LRMS_JOB_SCRIPT
echo "export HOME=\$RUNTIME_JOB_DIR" >> $LRMS_JOB_SCRIPT
##############################################################
# Skip execution if something already failed
##############################################################
echo "" >> $LRMS_JOB_SCRIPT
echo "if [ \"\$RESULT\" = '0' ] ; then" >> $LRMS_JOB_SCRIPT
echo "echo \"runtimeenvironments=\$runtimeenvironments\" >> \"\$RUNTIME_JOB_DIAG\"" >> $LRMS_JOB_SCRIPT
##############################################################
# Runtime configuration at computing node
##############################################################
RTE_stage1
#extra checks
if [ -z "$RUNTIME_NODE_SEES_FRONTEND" ] ; then
echo "Nodes detached from gridarea are not supported when LSF is used. Aborting job submit" 1>&2
rm -f "$LRMS_JOB_SCRIPT" "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
exit 1
fi
gate_host=`uname -n`
if [ -z "$gate_host" ] ; then
echo "Can't get own hostname" 1>&2
rm -f "$LRMS_JOB_SCRIPT" "$LRMS_JOB_OUT" "$LRMS_JOB_ERR"
exit 1
fi
##############################################################
# Execution
##############################################################
cd_and_run
##############################################################
# End of RESULT checks
##############################################################
echo "fi" >> $LRMS_JOB_SCRIPT
##############################################################
# Runtime (post)configuration at computing node
##############################################################
configure_runtime
#####################################################
# Upload output files
####################################################
if [ "$joboption_localtransfer" = 'yes' ] ; then
echo "UPLOADER=\${UPLOADER:-$basedir/uploader}" >> $LRMS_JOB_SCRIPT
cat >> $LRMS_JOB_SCRIPT <<'EOSCR'
if [ "$RESULT" = '0' ] ; then
$UPLOADER -p -c 'local' "$RUNTIME_CONTROL_DIR" "$RUNTIME_JOB_DIR" 2>>${RUNTIME_CONTROL_DIR}/job.local.errors
if [ $? -ne '0' ] ; then
echo 'ERROR: Uploader failed.' 1>&2
if [ "$RESULT" = '0' ] ; then RESULT=1 ; fi
fi
fi
rm -f "${RUNTIME_CONTROL_DIR}/job.local.proxy"
EOSCR
fi
##############################################################
# Move files back to session directory (job is done on node only)
# RUNTIME_JOB_DIR -> RUNTIME_LOCAL_SCRATCH_DIR/job_id
##############################################################
move_files_to_frontend
#######################################
# Submit the job
#######################################
# Execute bsub command
cd "$joboption_directory"
#chmod 0755 $LRMS_JOB_SCRIPT
# We make the assumption that $joboption_directory is locally available according to the requirements of any arc installation
echo "----------------- BEGIN job script -----" 1>&2
cat $LRMS_JOB_SCRIPT 1>&2
echo "----------------- END job script -----" 1>&2
${LSF_BSUB} < $LRMS_JOB_SCRIPT 1>$LRMS_JOB_OUT 2>$LRMS_JOB_ERR
if [ $? -eq '0' ] ; then
job_id=`cat $LRMS_JOB_OUT | awk '{split($0,field," ");print field[2]}' | sed 's/[<>]//g'`
if [ "${job_id}" = "" ] ; then
echo "job *NOT* submitted successfully!" 1>&2
echo "failed getting the jobid for the job!" 1>&2
else
echo "joboption_jobid=$job_id" >> $arg_file
echo "job submitted successfully!" 1>&2
echo "local job id: $job_id" 1>&2
# Remove temporary job script file
rm -f $LRMS_JOB_SCRIPT $LRMS_JOB_OUT $LRMS_JOB_ERR
echo "----- exiting submit_lsf_job -----" 1>&2
echo "" 1>&2
exit 0
fi
else
echo "job *NOT* submitted successfully!" 1>&2
echo "got error code from qsub!" 1>&2
fi
echo "Output is:" 1>&2
cat $LRMS_JOB_OUT 1>&2
echo "Error output is:"
cat $LRMS_JOB_ERR 1>&2
rm -f $LRMS_JOB_SCRIPT $LRMS_JOB_OUT $LRMS_JOB_ERR
echo "----- exiting submit_lsf_job -----" 1>&2
echo "" 1>&2
exit 1
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